Background The prevalence of atopic diseases has been increasing remarkably. The less frequent opportunities for infection early in life, especially mycobacteria exposure seem to parallel this higher prevalence of atopic diseases. We focused on BCG vaccination, performed by a multi-puncture method, which might play a role in the primary prevention of atopic diseases through Th1-promoting ability. Methods During a defined period, we mailed self-administered questionnaires to every household with a 3-year-old child consulting a local health center in Tokyo for routine developmental check-ups. The main questions concerned the existence of current physician-diagnosed atopic diseases (atopic dermatitis, bronchial asthma, and allergic rhinitis) requiring continuous medical management, the number of BCG scars (range; 0-18), and potential confounders such as gender, parental atopy, and environmental cofactors. Results Over the 12-month study period, 1, 105 (boys 49.5%) datasets were collected. The overall prevalence rates were 6.4% for atopic dermatitis, 4.3% for bronchial asthma, 4.2% for allergic rhinitis, and 12.1% for any of them. Most of the children had received BCG vaccination during the early months of life. The children with 15 or more BCG scars had a significantly lower prevalence of any atopic disease as compared to those with 4 scars or less (OR=0.52, 95%CI0.27-0.98). This association remained significant even after controlling for potential confounders. Conclusion A larger number of BCG scars was associated with less atopy development at age 3. Further studies are needed to clarify the causation.